[gmx-developers] /gromacs/bin.SSE2/gmx: not found

[fernando at hypernetlabs.io]

Thanks for the update Mark. Is there a way to circumvent this, in the interim, by passing a command, and environment variable, something to the image?

Thanks!

 

From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se <gromacs.org_gmx-developers-bounces at maillist.sys.kth.se> On Behalf Of Mark Abraham
Sent: Tuesday, April 14, 2020 1:17 AM
To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
Subject: Re: [gmx-developers] /gromacs/bin.SSE2/gmx: not found

 

Hi,

 

The container image got rebuilt automatically recently after some updates to the bioexcel gromacs-docker repo, and I saw it hasn't got the SIMD-specific builds in it that the container expects to find. But I haven't yet found out why.

 

Mark

 

On Mon, 13 Apr 2020 at 22:53, <fernando at hypernetlabs.io <mailto:fernando at hypernetlabs.io> > wrote:

Erik, happy to be the guinea pig! Just have to get other time-sensitive work out of the way and will look into this. I am no Gromacs/Docker expert (but I learn fast!) so it may take me a little longer than other guinea pigs in this listserv.

 

Will provide status update when there is one!

 

From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se <mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se>  <gromacs.org_gmx-developers-bounces at maillist.sys.kth.se <mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se> > On Behalf Of Erik Lindahl
Sent: Monday, April 13, 2020 1:57 PM
To: gmx-developers at gromacs.org <mailto:gmx-developers at gromacs.org> 
Cc: Discussion list for GROMACS development <gromacs.org_gmx-developers at maillist.sys.kth.se <mailto:gromacs.org_gmx-developers at maillist.sys.kth.se> >
Subject: Re: [gmx-developers] /gromacs/bin.SSE2/gmx: not found

 

Hi Fernando,

 

I have to confess that Windows isn't a normal target for us, but at least in theory that shouldn't matter for Docker :-)

 

Background: GROMACS has some very heavy CPU-specific optimization, so normally we use separate builds for SSE2, SSE4.1, AVX, AVX2, AVX512, etc. To make this work well with Docker, but also make sure you get the fastest possible binary, the Dockerfile actually builds all of these targets and installs them in separate directories, and then we check your CPU architecture at runtime, select the right CPU target, and execute the command in that subdirectory.

 

1) Can you check (in the container) what the contents of the directory /gromacs/bin.SSE2/ is?  (and any other bin.XXX directories under /gromacs)?

 

2) As far as I know, SSE2 should be one of the default builds, simply because it's the oldest possible platform we can imagine. However, it's pretty rare for a machine to actually be that old, so maybe our detection misses something on your windows machine. Do you know what CPU model you have?  If you can execute a shell in the container, doing "lscpu" might help us diagnose it!

 

Getting things to work well in Docker under Windows would be great, so if you don't mind being a guinea-pig we'll make sure to help you get it working :-)

 

Cheers,

 

Erik  

 

 

 

On Mon, Apr 13, 2020 at 8:34 PM <fernando at hypernetlabs.io <mailto:fernando at hypernetlabs.io> > wrote:

Good day all.

Using Docker Desktop and my Windows command prompt, I first successfully built the https://hub.docker.com/r/gromacs/gromacs image.

 

Successfully built d96a903309fa

Successfully tagged test5:latest

 

Then I used the following command “docker run --publish 8000:8080 --name ctest5 test5” to run a container from that image ‘test5’.

And the CLI printed the following “/gromacs/bin/gmx: 12: /gromacs/bin/gmx: /gromacs/bin.SSE2/gmx: not found”

 

Anyone has experienced the same that could provide some advice? Many thanks!

Fernando

+18147778447

 

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Erik Lindahl <erik.lindahl at dbb.su.se <mailto:erik.lindahl at dbb.su.se> >

Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm University

Science for Life Laboratory, Box 1031, 17121 Solna, Sweden

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